Chris my friend you really have a long way to go but i think in the end the result will be very satisfactory. As for your questions and since i'm trying to finish the same project in this period (as you might already know) i could tell you:
a) Pico psu to feed enough the little beast. I have had one installed and it works like a charm, no hangs and things like that (thanx Keropi :-) )
b)Bmon to change between Aga / Bvision but i don't know if you'll be able to track it down easily
c)Airflow is the most important for the system. I suppose heatsinks on all the Bvision chips and especially on the Permedia one which runs hot immediately. I have also closed all the upper case space and left some space exactly above Permedia along with a fan that pulls air out of the system. Then you should also take care of the PPC itself with a nice fan and heatsink at the trapdoor side (trapdoor should be removed permanently IMHO) and raise a little bit the Amiga case with rubber feet or sth like that.
d) Slimline cd should work without problems. With a Dremel or similar tool, a lot of patience and accuracy you could make the space for it. I have managed to open one on the left side of the case with no problems. Of course a slot load cd would be perfect (check out on Amigahellas.gr and even here if i remember well what Stromlord has done about it)
Of course all the above is to be done at our own risk and maybe someone else would object to it. I think mfilos (amigaplanet.gr) has done exactly the same with his 1200 but hasn't yet finished the project. Why don't you drop him a line? By now he could have closed the A1200 case if he found the time :-D :-D
